FAIRMol

Z29294093

Pose ID 12176 Compound 2981 Pose 655

DB fairmolDocking pose analysis is being read from this database.
Compound detail Protein structures Back to compounds
Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
T18
T. brucei TR (Mepacrine binding site (MBS, site 1)) T. brucei Mepacrine binding site (MBS, site 1)
Ligand Z29294093
PDB6RB5↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Promising SASA cached
Promising and worth follow-up
Binding strong Geometry high Native strong SASA done
Strain ΔE
18.2 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.69, Jaccard 0.50
Burial
66%
Hydrophobic fit
68%
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.772 kcal/mol/HA) ✓ Good fit quality (FQ -7.59) ✓ Good H-bonds (5 bonds) ✓ Deep burial (66% SASA buried) ✓ Lipophilic contacts well-matched (68%) ✗ Moderate strain (18.2 kcal/mol) ✗ Geometry warnings ✗ Minor protein-contact clashes (3) ✗ Internal clashes (8)
Score
-24.702
kcal/mol
LE
-0.772
kcal/mol/HA
Fit Quality
-7.59
FQ (Leeson)
HAC
32
heavy atoms
MW
492
Da
LogP
2.78
cLogP
Strain ΔE
18.2 kcal/mol
SASA buried
66%
Lipo contact
68% BSA apolar/total
SASA unbound
758 Ų
Apolar buried
340 Ų

Interaction summary

HB 5 HY 24 PI 2 CLASH 1

HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.

PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.

HY · Hydrophobic contacts

CLASH · Clashes
Final rank0.758Score-24.702
Inter norm-0.754Intra norm-0.018
Top1000noExcludedno
Contacts14H-bonds5
Artifact reasongeometry warning; 8 clashes; 3 protein contact clashes
Residues
CYS52 GLU18 GLY13 GLY49 ILE106 ILE339 LEU17 MET113 SER14 THR335 TRP21 TYR110 VAL53 VAL58

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name6RB5Contacts13
PoseOpen native poseHB0
IFP residues
ASP116 GLU18 GLY112 ILE106 LEU17 MET113 SER109 THR117 THR335 TRP21 TYR110 VAL53 VAL58
Current overlap9Native recall0.69
Jaccard0.50RMSD-
HB strict0Strict recall-
HB same residue+role0HB role recall-
HB same residue0HB residue recall-

Protein summary

493 residues
Protein targetT18Atoms7550
Residues493Chains1
Residue summaryVAL:768; LYS:704; LEU:703; ILE:532; GLU:450; THR:434; ARG:408; PHE:400; ALA:390; ASN:350; PRO:350; GLY:336; SER:319; TYR:294; ASP:276; MET:221

Receptor context

1 kept / 0 excluded
Receptor context filtering: interactions and SASA are computed against protein atoms plus allowed cofactors/ions. Native ligand-like HETATM partners are excluded from scoring.
Kept context 1 Excluded HETATM 0
Kept cofactors / ions
A:FAD501

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
636 0.36756071199063006 -0.995577 -29.8272 10 14 0 0.00 - - no Open
655 0.7583713310629582 -0.754114 -24.7022 5 14 9 0.69 - - no Current
654 2.399465623266646 -0.706171 -22.0319 8 15 0 0.00 - - no Open

Molecular metrics

RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
✓ Metrics available

Scoring & efficiency
Docking score -24.702kcal/mol
Ligand efficiency (LE) -0.7719kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.591
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 32HA

Physicochemical properties
Molecular weight 491.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.78
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 18.23kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 4.98kcal/mol
Minimised FF energy -13.25kcal/mol

SASA & burial

✓ computed
SASA (unbound) 757.6Ų
Total solvent-accessible surface area of free ligand
BSA total 499.9Ų
Buried surface area upon binding
BSA apolar 340.1Ų
Hydrophobic contacts buried
BSA polar 159.8Ų
Polar contacts buried
Fraction buried 66.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 68.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3141.9Ų
SASA_nonpolar(complex) − SASA_nonpolar(receptor) − SASA_nonpolar(ligand free). Negative = non-polar surface buried upon binding. Requires full polarity-decomposed SASA computation.
Receptor non-polar SASA 4076.6Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1472.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)